@article{Krejci2015,
  doi = {10.1093/bioinformatics/btv522},
  url = {https://doi.org/10.1093/bioinformatics/btv522},
  year = 2015,
  month = {sep},
  publisher = {Oxford University Press ({OUP})},
  pages = {btv522},
  author = {Adam Krejci and Ted R. Hupp and Matej Lexa and Borivoj Vojtesek and Petr Muller},
  title = {Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets},
  journal = {Bioinformatics}
}


@article{Soding2004,
  doi = {10.1093/bioinformatics/bti125},
  url = {https://doi.org/10.1093/bioinformatics/bti125},
  year  = {2004},
  month = {nov},
  publisher = {Oxford University Press ({OUP})},
  volume = {21},
  number = {7},
  pages = {951--960},
  author = {J. Soding},
  title = {Protein homology detection by {HMM}-{HMM} comparison},
  journal = {Bioinformatics}
}

@article{Kim2011,
  doi = {10.1093/nar/gkr1294},
  url = {https://doi.org/10.1093/nar/gkr1294},
  year  = {2011},
  month = {dec},
  publisher = {Oxford University Press ({OUP})},
  volume = {40},
  number = {6},
  pages = {e47--e47},
  author = {T. Kim and M. S. Tyndel and H. Huang and S. S. Sidhu and G. D. Bader and D. Gfeller and P. M. Kim},
  title = {{MUSI}: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets},
  journal = {Nucleic Acids Research}
}

@article{Crooks2004,
  doi = {10.1101/gr.849004},
  url = {https://doi.org/10.1101/gr.849004},
  year  = {2004},
  month = {may},
  publisher = {Cold Spring Harbor Laboratory},
  volume = {14},
  number = {6},
  pages = {1188--1190},
  author = {G. E. Crooks},
  title = {{WebLogo}: A Sequence Logo Generator},
  journal = {Genome Research}
}

@article{Giardine2005,
  doi = {10.1101/gr.4086505},
  url = {https://doi.org/10.1101/gr.4086505},
  year  = {2005},
  month = {sep},
  publisher = {Cold Spring Harbor Laboratory},
  volume = {15},
  number = {10},
  pages = {1451--1455},
  author = {B. Giardine},
  title = {Galaxy: A platform for interactive large-scale genome analysis},
  journal = {Genome Research}
}


@article{Finn2011,
  doi = {10.1093/nar/gkr367},
  url = {http://dx.doi.org/10.1093/nar/gkr367},
  year  = {2011},
  month = {may},
  publisher = {Oxford University Press ({OUP})},
  volume = {39},
  number = {suppl},
  pages = {W29--W37},
  author = {R. D. Finn and J. Clements and S. R. Eddy},
  title = {{HMMER} web server: interactive sequence similarity searching},
  journal = {Nucleic Acids Research}
}

@article{Sievers2011,
  doi = {10.1038/msb.2011.75},
  url = {http://dx.doi.org/10.1038/msb.2011.75},
  year  = {2011},
  month = {jan},
  publisher = {Wiley-Blackwell},
  volume = {7},
  number = {1},
  pages = {539--539},
  author = {F. Sievers and A. Wilm and D. Dineen and T. J. Gibson and K. Karplus and W. Li and R. Lopez and H. McWilliam and M. Remmert and J. Soding and J. D. Thompson and D. G. Higgins},
  title = {Fast,  scalable generation of high-quality protein multiple sequence alignments using Clustal Omega},
  journal = {Molecular Systems Biology}
}
